The Open Biomedical Ontologies (OBO) Foundry is a collaborative experiment: to produce well-structured vocabularies for shared use across different biological and medical domains. The OBO Foundry introduces a new paradigm for biomedical ontology development by the establishment of gold standard reference ontologies for individual domains of inquiry.

Back in 2002 Michael Ashburner and Suzanna Lewis initiated this grass-roots effort. The goal of OBO Foundry is to work with the community to create a suite of interoperable reference ontologies in the biomedical domain. We organize small content-development workshops to assist groups who have need of an ontology to support their research, such as anatomies, cell types, environments, and so on. From August 2005-2008 these workshops were supported through our 3-year collaboration with the National Center for Biomedical Ontology (NCBO).

Our Role

BBOP currently hosts the OBO foundry website and associated tools as a free service, such as nightly production of alternate ontology formats.

We perform continuous integration on a number of ontologies: http://build.berkeleybop.org

We are also involved in a number of ontology development efforts, such as:

  • GO: The Gene Ontology (see above)
  • RO: OBO Relations Ontology
  • Uberon: Uberon
  • EnvO: Environmental Ontology
  • PATO: OBO Phenotype Quality Ontology

Blog Posts

References

  • Ashburner, M., Mungall, C. J., & Lewis, S. E. (2003). Ontologies for biologists: a community model for the annotation of genomic data. In Cold Spring Harbor symposia on quantitative biology (Vol. 68, pp. 227–235).
  • Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., … Lewis, S. (2007). The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol, 25(11), 1251–1255. http://doi.org/10.1038/nbt1346
  • Mungall, C. J., Dietze, H., Carbon, S. J., Ireland, A., Bauer, S., & Lewis, S. (2012). Continuous Integration of Open Biological Ontology Libraries. Retrieved from http://bio-ontologies.knowledgeblog.org/405
  • Overton, J. A., Dietze, H., Essaid, S., Osumi-sutherland, D., & Mungall, C. J. (2015). ROBOT : A command-line tool for ontology development. In Proceedings of the International Conference on Biomedical Ontology (ICBO) (pp. 131–132). Lisbon, Portugal.
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